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An increased number of pancreatic cysts are being diagnosed due to the increased usage of cross-sectional imaging. Endoscopic ultrasound (EUS)-guided fine needle aspiration (FNA) cytology and molecular analysis of these cystic lesions have led to their better detection and characterization. The aim of this review is to assess the value of cyst fluid analysis for the differential diagnosis of pancreatic cystic lesions, in view of the recent progresses of molecular analysis methods. Pancreatic cysts can be either simple (retention) cysts, pseudocysts and cystic neoplasms, while these are further subdivided into serous cystadenomas, mucinous cystic neoplasms (MCNs) or intraductal papillary mucinous neoplasms (IPMNs). EUS is now being used to investigate cystic pancreatic lesions, particularly by means of EUS-guided cyst aspiration and sampling of the cyst wall or septa, as well as mural nodules. Cyst fluid can be further studied after aspiration in order to analyze cytology, viscosity, extracellular mucin, other tumor markers (CEA, CA 19-9, CA 15-3, Ca 72-4, etc.), enzymes (amylase, lipase), as well as DNA analysis of DNA quality/content or mutational analysis to study allelic imbalance/LOH (loss of heterozygosity) and K-ras mutations. After careful review of the published studies, a conclusion was reached that the use of tumor and molecular markers in conjunction with multimodality detection methods such as CT, MR and EUS-FNA allows risk stratification, while being also cost-effective. [ABSTRACT FROM AUTHOR]